My Research Highlights

I develop novel methods to solve complex biomedical challenges with big data,
including text, wet lab results, and clinical records.

NetRegMLR: Network-guided characterization of transcriptional drug response

Magical boost in regression performance from network guidance.

PI: Saurabh Sinha

SetSearch: Intelligent biomedical literature search engine for entity set queries

Proved superior performance over Google Scholar, PubMed and BM25.

PI: Jiawei Han

ALS progression prediction project brief illustration

ForestPaths: Personalized ALS progression prognosis by path tracking in random forests

The best model for Irish and Italian ALS patients in DREAM 2015.

PI: Jian Peng

Prostate cancer survival prediction project brief illustration

DWCox: Density-weighted Cox model for outlier-robust survival prognosis

A best survival model for prostate cancer in DREAM 2015.

PI: Jian Peng

My Background

I have a strong background in machine learning, data mining, biology, statistics, mathematics and physics. I have won numerous competitions, awards and scholarships whose monetary rewards sum up to over US$ 62,000.

Publications

Open-Domain Question Answering with Pre-Constructed Question Spaces

Jinfeng Xiao, Lidan Wang, Franck Dernoncourt, Trung Bui, Tong Sun, Jiawei Han
NAACL SRW 2021 [Paper]

SigMat: A Classification Scheme for Gene Signature Matching

Jinfeng Xiao, Charles Blatti, Saurabh Sinha
ISMB / Bioinformatics 2018 [Paper] [Code]

DWCox: A Density-Weighted Cox Model for Robust Prediction of Prostate Cancer Survival

Jinfeng Xiao, Sheng Wang, Jingbo Shang, Henry Lin, Doris Xin, Xiang Ren, Jiawei Han, Jian Peng
F1000Research 2016 [Paper] [Code]

ChemNER: Fine-Grained Chemistry Named Entity Recognition with Ontology-Guided Distant Supervision

Xuan Wang, Vivian Hu, Xiangchen Song, Shweta Garg, Jinfeng Xiao, Jiawei Han
EMNLP 2021 [Paper]

Fine-Grained Chemical Entity Typing with Multimodal Knowledge Representation

Chenkai Sun, Weijiang Li, Jinfeng Xiao, Nikolaus Parulian, Chengxiang Zhai, and Heng Ji
BIBM HiBB 2021 [Paper]

Scaling Up Data Science Course Projects: A Case Study

Bhavya Bhavya, Jinfeng Xiao and Chengxiang Zhai
L@S WiP 2021 [Paper]

Leveraging Personalized Sentiment Lexicons for Sentiment Analysis

Dominic Seyler, Jiaming Shen, Jinfeng Xiao, Yiren Wang, and ChengXiang Zhai
ICTIR 2020 [Paper]

Knowledge-Guided Analysis of "Omics" Data Using the KnowEnG Cloud Platform

Charles Blatti III et al.
PLoS Biology 2020 [Paper]

Query-Specific Knowledge Summarization with Entity Evolutionary Networks

Carl Yang, Lingrui Gan, Zongyi Wang, Jiaming Shen, Jinfeng Xiao and Jiawei Han
CIKM 2019 [Paper]

Stratification of Amyotrophic Lateral Sclerosis Patients: A Crowdsourcing Approach

Robert Kueffner et al.
Scientific Reports 2019 [Paper]

SetSearch+: Entity-Set-Aware Search and Mining for Scientific Literature

Jiaming Shen*, Jinfeng Xiao*, Yu Zhang, Carl Yang, Jingbo Shang, Jinda Han, Saurabh Sinha, Peipei Ping, Richard Weinshilboum, Zhiyong Lu and Jiawei Han
KDD 2018 [Preprint] [System]

Entity Set Search of Scientific Literature: An Unsupervised Ranking Approach

Jiaming Shen, Jinfeng Xiao, Xinwei He, Jingbo Shang, Saurabh Sinha, Jiawei Han
SIGIR 2018 [Paper]

Large-Scale Integration of Heterogeneous Pharmacogenomic Data for Identifying Drug Mechanism of Action

Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng
PSB 2018 [Paper]

DPPred: An Effective Prediction Framework with Concise Discriminative Patterns

Jingbo Shang, Meng Jiang, Wenzhu Tong, Jinfeng Xiao, Jian Peng, Jiawei Han
IEEE TKDE 2018 [Paper]

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

Justin Guinney et al.
Lancet Oncology 2017 [Paper]

Conference Presentations

Network-Guided Characterization of Drug-Specific Transcriptional Response in Cancer

Jinfeng Xiao, Charles Blatti, Saurabh Sinha
BD2K-LINCS Data Science Symposium 2017

Using Aggregated Weights Along Paths Across Random Forest to Select Important Features and Predict ALS Progression

Jinfeng Xiao, Jian Peng
RECOMB/ISCB RSG with DREAM 2015

Application of the Transition Probability Matrix to Colloidal Diffusion in a Periodic Energy Landscape

Jinfeng Xiao, Xiaoguang Ma, Penger Tong
Frontiers of Soft Matter Physics 2014

Kaleidoscope of Life

Here are ways I enjoy my time off.

Bridge the gap

I build connections between the UIUC community and the industry. I bring together not only students and employers, but also professors and industrial research funds. Companies benefited from my effort include Huawei, Alibaba, Dow, Jump Trading, TuSimple, etc.

Make cool videos and photos

I am a self-trained expert of multimedia editing. I can create short movies from photos and video clips, or make photos look better. I have made multiple videos for research groups and student organizations. I am also active on video publication websites like bilibili.

Reach hearts with words

I enjoy reading, and I am good at writing. My first paid job was as a magazine's editor when I was 10. The snapshot above is from my interview-based article (in Chinese) about a UIUC alumnus Xiaohuang Huang, now CEO of Exacloud, a high-tech startup.

Explore the world

I love experiencing the beauty of nature and human culture. Let's go travelling during the next break!

Sing it out

I love singing. I sing for fun, for expression of emotions, and for making friends. Let's go karaoke!

Move, move, move

I play many sports, like dancing, badminton, cycling, basketball, kendo, etc. Let's play together!